def erule(rule, domain):
def makeDiffusions(expression, dst):
for agent in expression:
if(interfaceHasSite(agent["interface"], "%")):
diffuseAgent(agent["interface"], dst)
def encloseAndSuffix(prefix, suffix):
return "(" + prefix + ") " + suffix
def mixRuleWithLoc(loc):
newRule = copy.deepcopy(rule)
newRule["label"] = newRule["label"].replace("%loc",loc)
checkForAlgebraicExpressions(newRule["lhs"],["%loc"],[locations[loc]],str(0))
checkForAlgebraicExpressions(newRule["rhs"],["%loc"],[locations[loc]],str(0))
solveAlgebraicExpressions(newRule["lhs"])
solveAlgebraicExpressions(newRule["rhs"])
newRule["lhs"] = checkForChains(newRule["lhs"])
newRule["rhs"] = checkForChains(newRule["rhs"])
insertLocInExpression(newRule["lhs"],loc)
insertLocInExpression(newRule["rhs"],loc)
newRule["rate"] = substituteDataArrayElementInString("%loc", newRule["rate"], locations[loc])
newRule["rate"] = newRule["rate"].replace("%loc", loc)
#if (isBimol(rule["lhs"])):
# newRule["rate"] = encloseAndSuffix(newRule["rate"], "/ " + str(locations[loc]))
return newRule
def mixRuleWithOrgDst(matrixCell):
(org, dst, r) = matrixCell
if (options.fullMatrix == False and r == 0):
return nullInstruction
if (org != dst):
newRule = copy.deepcopy(rule)
newRule["label"] = newRule["label"].replace("%org",org)
newRule["label"] = newRule["label"].replace("%dst",dst)
checkForAlgebraicExpressions(newRule["lhs"],[org,dst],[locations[org],locations[dst]], str(r))
checkForAlgebraicExpressions(newRule["rhs"],[org,dst],[locations[org],locations[dst]], str(r))
solveAlgebraicExpressions(newRule["lhs"])
solveAlgebraicExpressions(newRule["rhs"])
newRule["lhs"] = checkForChains(newRule["lhs"])
newRule["rhs"] = checkForChains(newRule["rhs"])
insertOrgInExpression(newRule["lhs"],org)
insertOrgInExpression(newRule["rhs"],org)
insertDstInExpression(newRule["lhs"],dst)
insertDstInExpression(newRule["rhs"],dst)
newRule["rate"] = substituteDataArrayElementInString("%org", newRule["rate"], locations[org])
newRule["rate"] = substituteDataArrayElementInString("%dst", newRule["rate"], locations[dst])
newRule["rate"] = newRule["rate"].replace("%cell", str(r))
newRule["rate"] = newRule["rate"].replace("%org", org)
newRule["rate"] = newRule["rate"].replace("%dst", dst)
#if (isBimol(rule["lhs"])):
# newRule["rate"] = encloseAndSuffix(newRule["rate"], "/ " + str(locations[org]))
makeDiffusions(newRule["rhs"], dst)
return newRule
else:
return nullInstruction
ruleBuilder = None
if (domain[0].__class__ == "".__class__): #if it is string, it is just loc
ruleBuilder = mixRuleWithLoc
else: #the type is tuple, it is a matrix
ruleBuilder = mixRuleWithOrgDst
for r in map(ruleBuilder, domain):
printing.printRule(r)